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Related Concept Videos

Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
Nucleosome Remodeling02:54

Nucleosome Remodeling

Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
The Nucleosome02:33

The Nucleosome

DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...
The Nucleosome02:33

The Nucleosome

DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...

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Related Experiment Video

Updated: May 13, 2026

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
06:02

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

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Taking into account nucleosomes for predicting gene expression.

Vladimir B Teif1, Fabian Erdel, Daria A Beshnova

  • 1Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum-DKFZ & BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. V.Teif@dkfz-heidelberg.de

Methods (San Diego, Calif.)
|March 26, 2013
PubMed
Summary
This summary is machine-generated.

Calculating transcription factor (TF) binding to DNA within nucleosomes is complex. This review discusses computational challenges and strategies for accurately predicting TF occupancy in chromatin to understand gene expression.

Keywords:
ChromatinCombinatorial bindingGene regulation functionProtein binding mapTF-nucleosome interference

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Detection of Post-translational Modifications on Native Intact Nucleosomes by ELISA

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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

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Detection of Post-translational Modifications on Native Intact Nucleosomes by ELISA
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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

Area of Science:

  • Molecular Biology
  • Genomics
  • Biophysics

Background:

  • Eukaryotic genomes organize DNA into nucleosomes, impeding transcription factor (TF) binding.
  • Accurate calculation of TF occupancy is crucial for predicting gene expression.

Purpose of the Study:

  • To review computational methods for calculating TF binding to nucleosomal DNA.
  • To address challenges in TF occupancy prediction within chromatin.

Main Methods:

  • Discusses theoretical problems including computation speed, chromatin remodeler activity, and model parameterization.
  • Reviews strategies to overcome these computational bottlenecks.

Main Results:

  • Identifies computational speed as a bottleneck for TF binding calculations.
  • Highlights the impact of chromatin remodelers on binding equilibrium.
  • Addresses challenges in parameterizing models from experimental data.

Conclusions:

  • Efficient computation of TF binding in chromatin requires addressing speed, remodeler activity, and parameterization.
  • Strategies are discussed to improve the accuracy of TF occupancy predictions.